Re: AMBER: Minimization and MD input files

From: Su Nwe <>
Date: Tue, 25 Sep 2007 13:25:19 -0700

Thanks you all for answering my questions.

This is the code I typed in for minization:
$AMBERHOME/exe/sander -o -i -o min_kelly.out -p
kelly.prmtop -c kelly.inpcrd -r min_kelly.rst

I added igb=6 and ntb=0 to my input file. ... (Thanks to David C. and
Carlos S :)

This is the error message I got (printed to terminal):
 mdfil: Error unknown flag:

     usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
-rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
mdinfo -radii radii]
Consult the manual for additional options.

Mr. Walker: I do not understand what you mean by this.
"How exactly are you running the minimizations - interactively or through a
queuing system?"

And I forgot to mention this: I'm running Amber 9 on Mac OS X 10.4.10

On 9/25/07, David A. Case <> wrote:
> On Tue, Sep 25, 2007, Su Nwe wrote:
> >
> > I'm trying to run a simple molecular dynamic "without solvent" on an
> > organic molecule using Amber 9. I could neither do minimization nor
> > molecular dynamics. I'm assuming that I made some errors in setting
> > parameters.
> >
> > The following is my minimization input file.
> > initial minimisation
> > &cntrl
> > imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=0
> > /
> The default in sander is ntb=1, that is, for a periodic box with solvent.
> If you want a simulation "without solvent", you need to specific ntb=0.
> >
> > I tried running the system "with solvent". Both minimization and
> > molecular dynamic works, but when I looked at the molecule (.mdcrd
> > file) using VMD, the molecules were shooting out everywhere and moving
> > so randomly.
> This sounds correct: if you want the animation to look "nice" (with all the
> molecules in the central unit cell,) you need to use the "image" command in
> ptraj to re-pack everything into the central unit cell.
> These may not be the only problems, but I hope they will get you going in the
> proper direction.
> ....dac
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Received on Wed Sep 26 2007 - 06:07:24 PDT
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